I only looked at the 6400 ISO, but I would say the RX1 performs slightly better; just a little bit more details. But to be honest I only can only see this at pixel level and a certain part e.g. the green napkin. This might be caused by the difference in exposure, but my guess is that the mirror causes a little bit micro-contrast lost.

I cannot see any difference when viewing the full size pictures, so I wouldn't worry about it. The advantage of the A99 over the RX1, should far outweight the 0.1% improvement e.g. speed and accuracy of AF.

I find the red swatch to have more detail in A99 sample @ISO6400. Anyway no surprise here, both are great cameras and there's barely any difference between the two. I am sure Sony refined further SLT technology, since A55.